A system and method of validating differences between measured values of fluorescence intensities obtained from a fluorescence-based instrument, including: generating calibration histograms for calibration beads run through the instrument; calibrating a distance function configured to measure distances between the histograms by: constructing a metric using the distance function, which includes a bin-to-bin dissimilarity matrix; and populating the dissimilarity matrix to maximize the following conditions: (A) the distance function of two histograms representing two sets of different beads equals the difference of their MESF values; and (B) the distance function of two histograms representing fluorescence of two sets of identical beads is zero; applying the metric to flow cytometry histograms generated for biological samples, to determine distances between the histograms; constructing a statistical test using the metric to determine a statistical significance of the distances; and determining whether the histogram results from the biological samples are reliable based on the statistical significance.